"The Missing Stories had always gone down very well and there was always a steady stream of interest in them, and so I was able to say 'Look, we can't afford to do audio dramas, we don't have the resources or the people to do them, this company [Big Finish Productions] do, let them do that, at the same time we can carry on our Doctor Who audio releases with the missing stories'. And so I'm happy to say that The Massacre will be coming out later this year, (...) and hopefully, if The Massacre goes well on CD and cassette, then the way will be open for further adventures to follow on afterwards..." [Steve Cole, speaking on DWMs "Talking 'Bout My Regeneration", 1999]

Beginning in 1999, this new range of missing episode soundtracks was produced and overseen by Mark Ayres, who took care to print the following disclaimer in each release, despite the excellent quality of the restored soundtracks:

The quality of the recording reflects the age of the material and the off-air nature of the source material. Whilst every attempt has been made to clean up and re-master these archive recordings using the latest technology, the sound quality may vary.

These releases were markedly better than all previous Doctor Who soundtracks, making full use of the CD format to present each story. Each release contained a full cast-listing, with dates of broadcast and a synopsis/production note. There were separate CD tracks for every scene, often resulting in short tracks when fast cutting takes place but allowing the listener unprecidented access to the story. (The booklet lists each track with the scene location and track length, e.g. Scene 5: TARDIS console room (00'46").) The episodes were generally narrated by a companion from the story (except for the re-releases of The Macra Terror, where, purely as an experiment, the original Missing Stories narration was reused), with scripts monitored and recorded by Mark Ayres; unlike the earlier Missing Stories releases, they are not performed in-character. Opening and closing title themes are replaced with the master copy of the relevant edit, with additional sound effects (such as the pulsating web in The Web Of Fear) or incidental music also dubbed from superior sources as appropriate. And every release is lovingly restored to the best possible quality, winning applause and admiration from reviewers and listeners alike.

Over the seven years from 1999-2006, every single missing story was restored and released on CD in this format. The range also included CD issues of radio stories Exploration Earth: The Time Machine, Slipback, The Paradise of Death, The Ghosts of N-Space, Death Comes to Time, Moths Ate My Doctor Who Scarf, the documentary Project: Who? and even the Genesis of the Daleks LP. Initially stories were chosen simply for their popularity, with partially-existing stories (such as The Moonbase and The Faceless Ones) pushed back in the schedules; but soon these were also available, narrated throughout, alongside stories where more episodes existed than were missing. (among them The Ice Warriors, The Reign of Terror, The Tenth Planet and The Invasion - the latter two released, rather apologetically, in a special cyberman tin.)

The range of missing adventures ended with The Reign of Terror in February 2006, but more releases were quickly scheduled: the intention being to create a range of fully narrated audio versions of popular or rare stories (particularly those with out-of-print video equivilents). "Audio is an entertainment format in its own right," commissioning editor Michael Stevens explained to SFX magazine in 2008, "with its own unique benefits: on the practical side, you can enjoy it when you’re driving, washing up or ironing, when you’re fell walking, marathon running or lying in bed with the lights off. On the aesthetic side, there’s something very special about enjoying a story – be it a novel, a drama or a sitcom – through the medium of sound alone. Spend a couple of hours in the company of William Russell as he narrates 'Marco Polo', or Frazer Hines on 'The Enemy of the World', and you’ll see what I mean. You get enveloped in the story. Plus, of course, the imagination compensates for any bugetary restrictions they might have had around sets, costumes and visual effects on TV! With audio, 'Marco Polo' really takes place in China, 'The Abominable Snowmen' in Tibet. And on our latest release, 'The Romans', the TARDIS crew really are lounging around eating grapes in an Italian villa – not sweltering under the arc lights in Lime Grove!" Thus the audiobooks continued with The Tomb of the Cybermen in May 2006 and remained a staple of the release schedules, mostly releasing vintage Hartnell, Troughton and Pertwee serials.

Some releases contained bonus tracks, including un-used Dalek dialogue (on Power of the Daleks), sound effects (Evil of the Daleks), original continuity announcements (The Daleks' Master Plan), occasional trailers for the following broadcast story (such as The Web of Fear trailer, which features at the end of The Enemy of the World CD), extra tracks of incidental music (The Gunfighters) and even a previously-unheard scene from The Monster of Peladon:1, reinstated from a studio recording. Both Marco Polo and The Daleks' Master Plan included CD-Rom content, with mp3s of the full-length episodes without their narration. And from the Cyberman Tin (Tenth Planet/The Invasion) onwards, each release contained a brief interview with the narrator, where they recalled their experiences of making that particular story and their thoughts on revisiting it for audio.

Several promotional give-aways were issued during the series' run. The first came in October 2001, free inside subscription and WHSmith copies of SFX Magazine #84, and contained the entire first-Doctor episode Mission to the Unknown in promotion of the recently-released Daleks' Master Plan 5-CD set. Another was attached to the cover of SFX Magazine: Special Edition #20 (a Doctor Who special) in March 2005. This bore the title Adventures in Time and Space and featured the complete first episode of Fury from the Deep, alongside extracts from 11 other releases.

The boxed set releases Daleks (in 2003) and Cybermen (in 2004) also contained exclusive single-CDs. The first, My Life as a Dalek, was a light-hearted and affectionate BBC Radio 4 documentary that had aired earlier that year, narrated by Mark Gattis and featuring clips from numerous Dalek stories alongside testimonies from - you guessed it - the actors who had voiced and been inside them. The other CD, Origins of the Cybermen, was a re-issue of a 1989 cassette recorded and produced by David Banks' company Silver Fist/Who Dares - an adapted reading of his own pseudo-history publication, The Cybermen, which re-told the Cybermen's story in chronological order.

This format was then repeated for BBC Audiobook's own pseudo-historical release, The Dalek Conquests, in May 2006. Clips from each and every televised Dalek story (including the 2005 episodes Dalek and Bad Wolf/The Parting of the Ways) were presented by Big Finish's Nicholas Briggs, in-character as a Dalek historian at Henry Van Statten's underground Utah museum. The CDs came part-way between talking book and television soundtrack, and trod much the same ground as 'My Life as a Dalek' and the BBC DVD documentary 'The Dalek Tapes' (released the same month on the Genesis of the Daleks DVD).